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3-Hydroxybutyryl-Coa Dehydrogenase from the Autotrophic 3-Hydroxypropionate/ 4-Hydroxybutyrate Cycle in Nitrosopumilus Maritimus

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3-Hydroxybutyryl-Coa Dehydrogenase from the Autotrophic 3-Hydroxypropionate/ 4-Hydroxybutyrate Cycle in Nitrosopumilus Maritimus fmicb-12-712030 June 29, 2021 Time: 18:32 # 1 ORIGINAL RESEARCH published: 05 July 2021 doi: 10.3389/fmicb.2021.712030 (S)-3-Hydroxybutyryl-CoA Dehydrogenase From the Autotrophic 3-Hydroxypropionate/ 4-Hydroxybutyrate Cycle in Nitrosopumilus maritimus Li Liu1, Daniel M. Schubert2, Martin Könneke3,4 and Ivan A. Berg1* 1 Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany, 2 Department of Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany, 3 Marine Archaea Group, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany, 4 Benthic Microbiology, Institute for Chemistry and Biology of the Marine Environments, University of Oldenburg, Oldenburg, Germany Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant organisms that exert primary control of oceanic and soil nitrification and are responsible for a large part of dark ocean primary production. They assimilate inorganic carbon via an energetically efficient version of the 3-hydroxypropionate/4- hydroxybutyrate cycle. In this cycle, acetyl-CoA is carboxylated to succinyl-CoA, which Edited by: is then converted to two acetyl-CoA molecules with 4-hydroxybutyrate as the key Johann Heider, University of Marburg, Germany intermediate. This conversion includes the (S)-3-hydroxybutyryl-CoA dehydrogenase Reviewed by: reaction. Here, we heterologously produced the protein Nmar_1028 catalyzing this Yejun Han, reaction in thaumarchaeon Nitrosopumilus maritimus, characterized it biochemically University of Chinese Academy of Sciences, China and performed its phylogenetic analysis. This NAD-dependent dehydrogenase is highly James F. Holden, active with its substrate, (S)-3-hydroxybutyryl-CoA, and its low Km value suggests that University of Massachusetts Amherst, the protein is adapted to the functioning in the 3-hydroxypropionate/4-hydroxybutyrate United States cycle. Nmar_1028 is homologous to the dehydrogenase domain of crotonyl-CoA *Correspondence: Ivan A. Berg hydratase/(S)-3-hydroxybutyryl-CoA dehydrogenase that is present in many Archaea. [email protected] Apparently, the loss of the dehydratase domain of the fusion protein in the course of evolution was accompanied by lateral gene transfer of 3-hydroxypropionyl-CoA Specialty section: This article was submitted to dehydratase/crotonyl-CoA hydratase from Bacteria. Although (S)-3-hydroxybutyryl- Microbial Physiology and Metabolism, CoA dehydrogenase studied here is neither unique nor characteristic for the HP/HB a section of the journal Frontiers in Microbiology cycle, Nmar_1028 appears to be the only (S)-3-hydroxybutyryl-CoA dehydrogenase in Received: 19 May 2021 N. maritimus and is thus essential for the functioning of the 3-hydroxypropionate/4- Accepted: 11 June 2021 hydroxybutyrate cycle and for the biology of this important marine archaeon. Published: 05 July 2021 Keywords: autotrophy, 3-hydroxypropionate/4-hydroxybutyrate cycle, Nitrosopumilus maritimus, ammonia- Citation: oxidizing archaea, Metallosphaera sedula, 3-hydroxybutyryl-CoA dehydrogenase Liu L, Schubert DM, Könneke M and Berg IA (2021) (S)-3-Hydroxybutyryl-CoA INTRODUCTION Dehydrogenase From the Autotrophic 3-Hydroxypropionate/ 4-Hydroxybutyrate Cycle Biological inorganic carbon fixation, the oldest and quantitatively most important biosynthetic in Nitrosopumilus maritimus. process in Nature, proceeds via at least seven natural pathways (Berg, 2011; Fuchs, 2011; Front. Microbiol. 12:712030. Sánchez-Andrea et al., 2020). Two of these pathways, the 3-hydroxypropionate/4-hydroxybutyrate doi: 10.3389/fmicb.2021.712030 (HP/HB) and the dicarboxylate/4-hydroxybutyrate (DC/HB) cycles were found only in Archaea Frontiers in Microbiology| www.frontiersin.org 1 July 2021| Volume 12| Article 712030 fmicb-12-712030 June 29, 2021 Time: 18:32 # 2 Liu et al. (S)-3-Hydroxybutyryl-CoA Dehydrogenase From Nitrosopumilus maritimus (Berg et al., 2010a). In both of these cycles, acetyl-CoA a C-terminal enoyl-CoA hydratase domain and an N-terminal is carboxylated to succinyl-CoA, which is then reduced to dehydrogenase domain (Ramos-Vera et al., 2011; Flechsler two acetyl-CoA molecules, regenerating the inorganic carbon et al., 2021). This protein is widespread among Archaea and acceptor and forming the final product of the cycle(s) was probably present in the last common ancestor of the (Figure 1). However, the carboxylation reactions are different. TACK-superphylum consisting of T haum-, A ig-, C ren-, and The carboxylases in the DC/HB cycle are ferredoxin-dependent Korarchaeota (Williams et al., 2017). Sulfolobales also possess pyruvate synthase and phosphoenolpyruvate carboxylase (Huber a homologous crotonyl-CoA hydratase/(S)-3-hydroxybutyryl- et al., 2008; Ramos-Vera et al., 2009), while a promiscuous CoA dehydrogenase. Although this protein is present in acetyl-CoA/propionyl-CoA carboxylase catalyzes both acetyl- autotrophically grown Metallosphaera sedula (Sulfolobales) cells CoA and propionyl-CoA carboxylations in the HP/HB cycle (Ramos-Vera et al., 2011; Liu et al., 2021), it is responsible (Chuakrut et al., 2003; Hügler et al., 2003). In the latter case, a only for a minute flux in the crotonyl-CoA conversion to number of specific enzymes are responsible for the conversion acetoacetyl-CoA in this archaeon (Liu et al., 2020, 2021). In of malonyl-CoA, the product of the acetyl-CoA carboxylase contrast to the organisms using the DC/HB cycle, M. sedula and reaction, to propionyl-CoA, which is then carboxylated and other Sulfolobales possess stand-alone crotonyl-CoA hydratase isomerized to succinyl-CoA (Figure 1). Further metabolism and (S)-3-hydroxybutyryl-CoA dehydrogenase enzymes in the of succinyl-CoA is identical in both cycles. Succinyl-CoA HP/HB cycle (Liu et al., 2020). Their crotonyl-CoA hydratase is reduction leads to the formation of 4-hydroxybutyrate, which is a promiscuous protein that has also a high 3-hydroxypropionyl- converted to 4-hydroxybutyryl-CoA and dehydrated to crotonyl- CoA dehydratase activity and thus catalyzes two (de)hydratase CoA. Crotonyl-CoA conversion to two acetyl-CoA molecules reactions in the cycle (Liu et al., 2021). Thaumarchaeota proceeds through the reactions known from b-oxidation: also use a similar promiscuous enzyme to catalyze these two hydration of crotonyl-CoA to (S)-3-hydroxybutyryl-CoA, its reactions (Liu et al., 2021). Interestingly, crenarchaeal and oxidation to acetoacetyl-CoA and cleavage to two acetyl-CoA thaumarchaeal 3-hydroxypropionyl-CoA dehydratases/crotonyl- molecules (Figure 1). CoA hydratases are closely related to bacterial enoyl-CoA The DC/HB cycle functions in anaerobic Crenarchaeota of hydratases but were retrieved independently by the ancestors of the orders Desulfurococcales and Thermoproteales (Huber et al., Sulfolobales and AOA from different bacteria (Liu et al., 2021). 2008; Ramos-Vera et al., 2009; Berg et al., 2010b), while the Here, we characterize (S)-3-hydroxybutyryl-CoA dehydrogenase HP/HB cycle is present in aerobic Sulfolobales (Crenarchaeota) from the ammonia-oxidizing thaumarchaeon Nitrosopumilus and ammonia-oxidizing Thaumarchaeota (AOA) (Ishii et al., maritimus, compare it with the enzyme from M. sedula 1997; Berg et al., 2007, 2010a; Könneke et al., 2014). For both and with the crotonyl-CoA hydratase/(S)-3-hydroxybutyryl-CoA cycles, variants exist. Although it appears that the cycles in dehydrogenases, and discuss the enzymological differences in Thermoproteales and Desulfurococcales evolved from a common these conversions in course of the DC/HB and HP/HB cycles. ancestor, the representatives of these two orders use a number of phylogenetically unrelated enzymes (e.g., succinyl-CoA reductase, succinic semialdehyde reductase) (Huber et al., 2008; MATERIALS AND METHODS Ramos-Vera et al., 2009; Flechsler et al., 2021). For the HP/HB cycle, two fundamentally different variants function in Cren- and Materials in Thaumarchaeota. The thaumarchaeal variant uses ADP/Pi- Chemicals and biochemicals were obtained from AppliChem producing 3-hydroxypropionyl-CoA and 4-hydroxybutyryl-CoA (Darmstadt, Germany), Cell Signaling Technology (Frankfurt, synthetases, while non-homologous synthetases produce AMP Germany), Fluka (Neu-Ulm, Germany), IBA (Göttingen, and PPi in the crenarchaeal HP/HB cycle in the corresponding Germany), Merck (Darmstadt, Germany), Roth (Karlsruhe, reactions (Berg et al., 2007; Hawkins et al., 2013, 2014; Germany), Sigma-Aldrich (Deisenhofen, Germany), or VWR Könneke et al., 2014). The usage of ADP-producing synthetases (Darmstadt, Germany). Materials for cloning and expression makes the thaumarchaeal HP/HB cycle the energetically most were purchased from Bioline (London, United Kingdom), efficient aerobic autotrophic pathway (Könneke et al., 2014). MBI Fermentas (St. Leon-Rot, Germany), New England The characteristic enzymes of these two variants of the cycle Biolabs (Frankfurt, Germany), or Novagen (Schwalbach, are mostly phylogenetically unrelated, implying the involvement Germany). Materials and equipment for protein purification of convergent evolution in their emergence (Berg et al., 2007; were obtained from Cytiva (Freiburg, Germany), Macherey- Könneke et al., 2014; Otte et al., 2015). Nagel (Düren, Germany), Millipore (Eschborn, Germany), Both DC/HB and HP/HB cycles (and all their variants) Pall Corporation (Dreieich, Germany), or Thermo Scientific have in common that crotonyl-CoA is converted to acetoacetyl- (Rockford, United States). Primers were synthesized by CoA (Figure
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